[gmx-users] Re: Seeking solution for the error "Atom OXT in residue TRP 323 was not found in rtp entry TRP with 24 atoms while sorting atoms".

[Tsjerk Wassenaar]

Hi Santhosh,

Try renaming the atom (mind the space):

sed 's/OXT/O2 /' pdbfile > fixed.pdb

And then run pdb2gmx on that.

Cheers,

Tsjerk


On Tue, Sep 17, 2013 at 6:05 AM, Santhosh Kumar Nagarajan <
santhoshrajan90 at gmail.com> wrote:

>
> This is the command I used
> pdb2gmx -f protein.pdb -o processed.gro -water spce -ignh
>
> And I used OPLS-AA/L all-atom force field..
>
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.